Since Fire Emblem has been around for more than 20 years, the script writers have managed to slip dirty innuendos in the dialogue more than once. The absolute winner is Fire Emblem Awakening, the newest (as of 2013) entry in the franchise:
Fire Emblem: Blazing Sword (or just Fire Emblem in the States) has some dark moments for an E-rated game. Specifically, the ending you get when Bartre and Karla are paired; Karla dies of illness after giving birth to Fil/Fir. Bartre "takes their daughter to her uncle and joins Karla."
This might actually be a Dub Induced Plothole ...but given that there were no plans to release fire emblem 6 out here, they figured they'd probably rather just imply that than state what really happened - Bartre is alive and well in Fire Emblem 6.
Though there is a more genuine example in Eliwood and Ninian's C support:
Eliwood: Hrm... Ah, I know! Next time you are free, show me your dancing! Not one of the little dances— something special.
In a DLC chapter, Nowi contemplates Tharja's boingy bits and feels her up. Yes, this is in the American version (though it didn't get past the European radar, as they changed it to Nowi discussing Tharja's hair)
Nowi (paraphrased): "You're the biggest one. Trust me!"
In the Future Past DLC, Grima in The Avatar's body taunts Lucina via mentioning how much her father Chrom was loved by the Avatar, aka the person who owned the body he's inhabiting. The catch here is that the dialogue does not really change either when a female Avatar is married to someone else than Chrom... or even more so, when the Avatar is a male (and maybe even Lucina's boyfriend/husband). That Chrom dude is damn popular with girlsand guys, isn't he?